If you're using openssl_pkey_new() in conjunction with openssl_csr_new() and want to change the CSR digest algorithm as well as specify a custom key size, the configuration override should be defined once and sent to both functions:

Although openssl_pkey_new() will accept the 'digest_alg' argument it won't use it, and setting the value has no effect unless you also set this value for openssl_csr_new(). The reason for this is that the $config array is acting as a drop-in replacement for the values found in the openssl.cnf file, so it must contain all of the override values that you need even if the function they're being sent to won't use them.

Also, if you change the 'digest_alg' to something like 'sha256' and still get an MD5 signed CSR check your openssl.cnf file to see whether the digest algorithm you want to use is actually supported.

Getting the public key corresponding to a particular private key, through the methods provided for by OpenSSL, is a bit cumbersome. An easier way to do it is to use phpseclib, a pure PHP RSA implementation: